Immcantation - enchantR
File size tracker
Updated: Tue Jan 28 16:42:19 2025
1 Input parameters
1.1 Log files loaded
- SRR1383451_add-meta_command_log.txt
- SRR1383451_changeo_assigngenes_command_log.txt
- SRR1383451_collapse_command_log.txt
- SRR1383451_fq_command_log.txt
- SRR1383451_jmod3_command_log.txt
- SRR1383451_makedb_command_log.txt
- SRR1383451_split_command_log.txt
- SRR1383452_add-meta_command_log.txt
- SRR1383452_changeo_assigngenes_command_log.txt
- SRR1383452_collapse_command_log.txt
- SRR1383452_fq_command_log.txt
- SRR1383452_jmod3_command_log.txt
- SRR1383452_makedb_command_log.txt
- SRR1383452_split_command_log.txt
- SRR1383453_add-meta_command_log.txt
- SRR1383453_changeo_assigngenes_command_log.txt
- SRR1383453_collapse_command_log.txt
- SRR1383453_fq_command_log.txt
- SRR1383453_jmod3_command_log.txt
- SRR1383453_makedb_command_log.txt
- SRR1383453_split_command_log.txt
- SRR1383456_add-meta_command_log.txt
- SRR1383456_changeo_assigngenes_command_log.txt
- SRR1383456_collapse_command_log.txt
- SRR1383456_fq_command_log.txt
- SRR1383456_jmod3_command_log.txt
- SRR1383456_makedb_command_log.txt
- SRR1383456_split_command_log.txt
- SRR1383463_add-meta_command_log.txt
- SRR1383463_changeo_assigngenes_command_log.txt
- SRR1383463_collapse_command_log.txt
- SRR1383463_fq_command_log.txt
- SRR1383463_jmod3_command_log.txt
- SRR1383463_makedb_command_log.txt
- SRR1383463_split_command_log.txt
- SRR1383464_add-meta_command_log.txt
- SRR1383464_changeo_assigngenes_command_log.txt
- SRR1383464_collapse_command_log.txt
- SRR1383464_fq_command_log.txt
- SRR1383464_jmod3_command_log.txt
- SRR1383464_makedb_command_log.txt
- SRR1383464_split_command_log.txt
- SRR1383465_add-meta_command_log.txt
- SRR1383465_changeo_assigngenes_command_log.txt
- SRR1383465_collapse_command_log.txt
- SRR1383465_fq_command_log.txt
- SRR1383465_jmod3_command_log.txt
- SRR1383465_makedb_command_log.txt
- SRR1383465_split_command_log.txt
- SRR1383466_add-meta_command_log.txt
- SRR1383466_changeo_assigngenes_command_log.txt
- SRR1383466_collapse_command_log.txt
- SRR1383466_fq_command_log.txt
- SRR1383466_jmod3_command_log.txt
- SRR1383466_makedb_command_log.txt
- SRR1383466_split_command_log.txt
- SRR1383467_add-meta_command_log.txt
- SRR1383467_changeo_assigngenes_command_log.txt
- SRR1383467_collapse_command_log.txt
- SRR1383467_fq_command_log.txt
- SRR1383467_jmod3_command_log.txt
- SRR1383467_makedb_command_log.txt
- SRR1383467_split_command_log.txt
- SRR1383468_add-meta_command_log.txt
- SRR1383468_changeo_assigngenes_command_log.txt
- SRR1383468_collapse_command_log.txt
- SRR1383468_fq_command_log.txt
- SRR1383468_jmod3_command_log.txt
- SRR1383468_makedb_command_log.txt
- SRR1383468_split_command_log.txt
3 File processing
3.1 SRR1383452_db-pass.tsv
3.1.2 Barplot
Number of reads at different stages of the processing of SRR1383452_db-pass.tsv File can be found here: SRR1383452_db-pass.tsv
ggplot file: SRR1383452_db-pass.RData
3.2 SRR1383464_db-pass.tsv
3.2.2 Barplot
Number of reads at different stages of the processing of SRR1383464_db-pass.tsv File can be found here: SRR1383464_db-pass.tsv
ggplot file: SRR1383464_db-pass.RData
3.3 SRR1383451_quality-pass.tsv
3.3.2 Barplot
Number of reads at different stages of the processing of SRR1383451_quality-pass.tsv File can be found here: SRR1383451_quality-pass.tsv
ggplot file: SRR1383451_quality-pass.RData
3.4 SRR1383467_meta-pass.tsv
3.4.2 Barplot
Number of reads at different stages of the processing of SRR1383467_meta-pass.tsv File can be found here: SRR1383467_meta-pass.tsv
ggplot file: SRR1383467_meta-pass.RData
3.5 SRR1383453_igblast.fmt7
3.5.2 Barplot
Number of reads at different stages of the processing of SRR1383453_igblast.fmt7 File can be found here: SRR1383453_igblast.tsv
ggplot file: SRR1383453_igblast.RData
3.6 SRR1383456_junction-pass.tsv
3.6.2 Barplot
Number of reads at different stages of the processing of SRR1383456_junction-pass.tsv File can be found here: SRR1383456_junction-pass.tsv
ggplot file: SRR1383456_junction-pass.RData
3.7 SRR1383466_meta-pass.tsv
3.7.2 Barplot
Number of reads at different stages of the processing of SRR1383466_meta-pass.tsv File can be found here: SRR1383466_meta-pass.tsv
ggplot file: SRR1383466_meta-pass.RData
3.8 SRR1383468_db-pass.tsv
3.8.2 Barplot
Number of reads at different stages of the processing of SRR1383468_db-pass.tsv File can be found here: SRR1383468_db-pass.tsv
ggplot file: SRR1383468_db-pass.RData
3.9 SRR1383465_igblast.fmt7
3.9.2 Barplot
Number of reads at different stages of the processing of SRR1383465_igblast.fmt7 File can be found here: SRR1383465_igblast.tsv
ggplot file: SRR1383465_igblast.RData
3.10 SRR1383463_meta-pass.tsv
3.10.2 Barplot
Number of reads at different stages of the processing of SRR1383463_meta-pass.tsv File can be found here: SRR1383463_meta-pass.tsv
ggplot file: SRR1383463_meta-pass.RData
4 Final table
Figure 4.1: Number of sequences at each processing step. ggplot file: sequence_count_plot.RData
5 Software versions
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-redhat-linux-gnu
## Running under: Fedora Linux 40 (Container Image)
##
## Matrix products: default
## BLAS/LAPACK: FlexiBLAS OPENBLAS-OPENMP; LAPACK version 3.11.0
##
## locale:
## [1] C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] plotly_4.10.4 ggplot2_3.5.1 tidyr_1.3.1 dplyr_1.1.4
## [5] enchantr_0.1.19
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-9 airr_1.5.0
## [3] gridExtra_2.3 rlang_1.1.4
## [5] magrittr_2.0.3 clue_0.3-66
## [7] GetoptLong_1.0.5 ade4_1.7-22
## [9] matrixStats_1.4.1 compiler_4.4.2
## [11] png_0.1-8 vctrs_0.6.5
## [13] stringr_1.5.1 pkgconfig_2.0.3
## [15] shape_1.4.6.1 crayon_1.5.3
## [17] fastmap_1.2.0 XVector_0.46.0
## [19] labeling_0.4.3 ggraph_2.2.1
## [21] utf8_1.2.4 Rsamtools_2.22.0
## [23] rmarkdown_2.29 tzdb_0.4.0
## [25] UCSC.utils_1.2.0 purrr_1.0.2
## [27] xfun_0.49 zlibbioc_1.52.0
## [29] cachem_1.1.0 seqinr_4.2-36
## [31] GenomeInfoDb_1.42.0 jsonlite_1.8.9
## [33] progress_1.2.3 DelayedArray_0.32.0
## [35] BiocParallel_1.40.0 tweenr_2.0.3
## [37] parallel_4.4.2 prettyunits_1.2.0
## [39] cluster_2.1.6 R6_2.5.1
## [41] bslib_0.8.0 stringi_1.8.4
## [43] RColorBrewer_1.1-3 jquerylib_0.1.4
## [45] GenomicRanges_1.58.0 bookdown_0.41
## [47] knitr_1.49 Rcpp_1.0.13-1
## [49] SummarizedExperiment_1.36.0 iterators_1.0.14
## [51] readr_2.1.5 IRanges_2.40.0
## [53] Matrix_1.7-1 igraph_2.1.1
## [55] tidyselect_1.2.1 rstudioapi_0.17.1
## [57] abind_1.4-8 yaml_2.3.10
## [59] viridis_0.6.5 doParallel_1.0.17
## [61] codetools_0.2-20 lattice_0.22-6
## [63] tibble_3.2.1 Biobase_2.66.0
## [65] withr_3.0.2 evaluate_1.0.1
## [67] polyclip_1.10-7 circlize_0.4.16
## [69] Biostrings_2.74.0 pillar_1.9.0
## [71] MatrixGenerics_1.18.0 DT_0.33
## [73] foreach_1.5.2 stats4_4.4.2
## [75] generics_0.1.3 S4Vectors_0.44.0
## [77] hms_1.1.3 munsell_0.5.1
## [79] scales_1.3.0 glue_1.8.0
## [81] lazyeval_0.2.2 tools_4.4.2
## [83] data.table_1.16.2 GenomicAlignments_1.42.0
## [85] graphlayouts_1.2.1 tidygraph_1.3.1
## [87] grid_4.4.2 ape_5.8
## [89] crosstalk_1.2.1 colorspace_2.1-1
## [91] nlme_3.1-166 GenomeInfoDbData_1.2.13
## [93] ggforce_0.4.2 cli_3.6.3
## [95] alakazam_1.3.0 fansi_1.0.6
## [97] S4Arrays_1.6.0 viridisLite_0.4.2
## [99] ComplexHeatmap_2.18.0 gtable_0.3.6
## [101] sass_0.4.9 digest_0.6.37
## [103] BiocGenerics_0.52.0 SparseArray_1.6.0
## [105] ggrepel_0.9.6 rjson_0.2.23
## [107] htmlwidgets_1.6.4 farver_2.1.2
## [109] memoise_2.0.1 htmltools_0.5.8.1
## [111] lifecycle_1.0.4 httr_1.4.7
## [113] GlobalOptions_0.1.2 MASS_7.3-61